Question: Problem with .vcf annovar
gravatar for A
11 months ago by
A3.7k wrote:


I faced a problem

I am trying to annotate my .vcf files by annovar to get maf as by maf I am able to visualize and do many things. I tried both vcf 4.1 and 4.2

[fi1d18@cyan01 annovar]$ my.vcf humandb/ -buildver hg19 -out myanno -remove -protocol refGene,cytoBand,exac03,avsnp147,dbnsfp30a -operation gx,r,f,f,f -nastring . -csvout -polish -xref example/gene_xref.txt

Annovar returns empty annotation

I tried to convert my vcf in annovar but I got

[fi1d18@cyan01 annovar]$ -format vcf4 /tmy.vcf  > ex2.avinput                                 WARNING to old ANNOVAR users: this program no longer does line-to-line conversion for multi-sample VCF files. If you want to include all variants in output, use '-format vcf4old' or use '-format vcf4 -allsample -withfreq' instead.
Error: invalid record in VCF file: the GT specifier is not present in the FORMAT string: <1       10445   .       A       G       .       LowEVS  SOMATIC;QSS=1;TQSS=1;NT=ref;QSS_NT=1;TQSS_NT=1;SGT=AA->AA;DP=562;MQ=23.95;MQ0=232;ReadPosRankSum=0.46;SNVSB=0.00;SomaticEVS=0.10    DP:FDP:SDP:SUBDP:AU:CU:GU:TU    69:29:1:0:38,261:2,14:0,4:0,4     38:16:0:0:20,168:0,7:2,7:0,1>

I tried online annovar says I got the same error

I really need a maf file from my .vcf files

I don't know what is the solution? Converting vcf 4.1 to 4 compatible with annovar?

Any help please?

maf annovar vcf • 688 views
ADD COMMENTlink modified 11 months ago by onemoreuser20 • written 11 months ago by A3.7k
gravatar for A
11 months ago by
A3.7k wrote:

I found that is okay with converting .vcf files coming from Mutect, VarScan, Delly even vcf 4.1 but not vcf 4.1 coming from Strelka. So because my variant caller was Strelka I was getting error. May be the easiest way for getting maf rom .vcf is vcf2maf but for that I needed to locate my data in VEP, I was not able to bind my data to the path to where VEP had been installed so I had to use Annovar for getting maf.

ADD COMMENTlink written 11 months ago by A3.7k
gravatar for onemoreuser
11 months ago by
onemoreuser20 wrote:

Did you try Ensembl VEP online? It´s easy to use and you get MAF as output by default.

ADD COMMENTlink written 11 months ago by onemoreuser20

I don't need VEP itself rather I needed getting maf file for getting mutational visualization but vcf2maf tool needs VEP, I had installed VEP but I was getting this error says fasta file missing from vep

ADD REPLYlink written 11 months ago by A3.7k
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